Run a simple benchmark

The Apoa1 example is a standard NAMD cross-platform benchmark. For more information on the Apoa1 example, see the NAMD website.

To run the Apoa1 example:

  1. Download the Apoa1 example:

    wget http://www.ks.uiuc.edu/Research/namd/utilities/apoa1.tar.gz
  2. Unpack the example:

    tar -xf apoa1.tar.gz
  3. Edit the Apoa1 deck file apoa1.namd, which is located in the unpacked apoa1 directory, to:

    1. Define the full path of the output directory to print to.

    2. Disable the use of FFTW wisdom (the FFTW interface for Arm Performance Libraries does not generate or utilize the FFTW wisdom files).

    using:

    1. outputname /path/to/Apoa1_output_dir/
    2. FFTWEstimate yes
      FFTWUseWisdom no
  4. Configure and run the example, using:

    NP=16
    ${INSTALL_DIR}/namd2 +p${NP} apoa1/apoa1.namd +setcpuaffinity

    Note:

    Set the number of processors according to your own system availability. In this example, we have run on 16 cores (NP=16).

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